Exploring the Genomic Diversity of Remote Islands using Ancient DNA

The beautiful islands of Southeast Asia comprise some of the most biodiversity rich regions globally. Genetically diverse species have adorned these islands for millions of years. What factors contributed to the genomic composition of birds on these islands? The problem is challenging to address, due to extensive loss of biodiversity and remote nature of many smaller islands across Southeast Asia. To date, museum collections from tropical regions were rarely used to address this problem due to sample degradation in the hot and humid climate. However, a new collaborative study involving biology researchers at Ashoka University have successfully addressed this problem and provided a possible evolutionary scenario regarding movement of birds across islands. 

The present-day islands in Southeast Asia such as Java, Peninsular Malaysia, Borneo, amongst others were all interconnected as one big landmass thousands of years ago. Earth’s climate has been experiencing cycles of global warming and cooling for the past 2.6 million years. During cooling cycles as ice forms, the sea level drops, creating land bridges between islands. While existing theories predict that geographical distance of islands from the mainland would determine genetic connectivity and evolutionary closeness, researchers from the current study find that rather than distance to the mainland, ancient land bridges and river barriers affected the genetic biodiversity of two songbirds in Southeast Asian islands. 

Left: Land bridges connecting Southeast Asian Islands; Right: Representative image of a River Barrier

The researchers studied ancient bird samples collected during 1893-1957 housed at the Lee Kong Chian Natural History Museum, Singapore. Researchers performed DNA analysis by carefully isolating DNA from toe pads of the birds. Although the museum collection was highly degraded, researchers could successfully collect and analyse the DNA using next-generation sequencing methods. Information obtained from DNA was used to trace the genomic      biodiversity of the songbirds. To understand the genomic diversity of birds on remote islands, researchers studied the effect of ancient land bridges by measuring underwater depth (Bathymetry) and also considered the potential role of ancient river barriers (paleo-rivers). The study shows that the birds on the small island were genetically similar to Peninsular Malaysia rather than Borneo, even though the islands were physically closer to Borneo. This may be due to the difference in the timing of land bridge formation and presence of ancient river barriers. 

According to previous theories, island biodiversity was mainly governed by distance to the mainland. This study reveals that ancient land bridges and river barriers influenced the genetic biodiversity of songbirds in Southeast Asian islands. Through this study, the researchers showed that museum collections are extremely important to understand evolution and genetic biodiversity. The approach used by Kritika Garg, Balaji Chattopadhyay and colleagues has proven to be very efficient and can be used to study highly degraded samples from tropical regions. This study opens multiple directions to explore the ancient roots of rich biodiversity in India.

The past climatic fluctuations have had a strong impact on the biodiversity of the Indian subcontinent. This is generally a neglected topic of research with only a few research groups focusing on understanding the impacts of climate change and how past human activities have shaped the current diversity. Kritika Garg is a faculty fellow at the Centre for Interdisciplinary Archaeological Research (CIAR) at Ashoka University.  She is an expert in ancient DNA isolation and analysis and is trying to understand the evolution of species across time scales.  To support this kind of research, the laboratory facilities at CIAR will include analysis of objects, excavation sites, and biological material using cutting-edge techniques from chemistry, biology, and physics. The facilities will aim to have archaeogenetic analysis of ancient DNA, physical and chemical dating methods, non-destructive imaging techniques, and more. To further support this research at an interface of archaeology and biology, the centre will house advanced microscopes, a clean room facility, instruments for nucleic acid extraction along with other necessary equipment. 

The Centre for Interdisciplinary Archaeological Research (CIAR), the first of its kind in India aims to create a state-of-the-art facility that brings archaeology and the sciences together to offer new perspectives and develop deep understanding of the Indian past. It aims to achieve this through interdisciplinary field-based projects led by the faculty and students at Ashoka University along with off-site laboratory work. The Centre will soon appoint more faculty to provide an evidence-based narrative of the Indian past, explore the evolution of infectious disease dynamics and their role in shaping the Indian civilization, understand our evolving relationship with nature and the surrounding environment to name a few. These discoveries will help frame policies to protect our archaeological sites, our response to climate change, deforestation and environmental degradation, and address the societal problems in a more integrated and holistic manner.

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Reference article: Island Biogeography Revisited: Museomics Reveals Affinities of Shelf Island Birds Determined by Bathymetry and Paleo-Rivers, Not by Distance to Mainland, Molecular Biology and Evolution, Volume 39, Issue 1, January 2022

Authors of the research article

Kritika M. Garg* – Department of Biological Sciences, National University of Singapore, Singapore, Centre for Interdisciplinary Archaeological Research, Ashoka University, Sonipat, India, Department of Biology, Ashoka University, Sonipat, India

Balaji Chattopadhyay – Department of Biological Sciences, National University of Singapore, Singapore, Trivedi School of Biosciences, Ashoka University, Sonipat, India

Emilie Cros – Department of Biological Sciences, National University of Singapore, Singapore 

Suzanne Tomassi – Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom

Suzan Benedick – Faculty of Sustainable Agriculture, University of Malaysia, Sabah, Malaysia

David P. Edwards – Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom

Frank E. Rheindt* – Department of Biological Sciences, National University of Singapore, Singapore

* Corresponding Authors